Lets start with the second item first. Welcome to the Microsoft freedom to innovate. Despite it not being included in the email specifications Microsoft in their corporate wisdom decided that if you send an email on their service you have to have a copy in your mail account. Hence Thunderbird makes a copy and so does Microsoft. Fun hey. But at least Thunderbird lets you turn of the copy in account settings > copies and folders. Microsoft offers no such setting.

Now the first. It might be a little less straight forward. Generally speaking people use IMAP and with that changes are synchronized across multiple devices using the same account. SO in that situation deletions from say a phone will show up as you describe in Thunderbird as a mail appearing and them "just moving" somewhere else.

That the mail is moving to a "local" junk folder leaves me thinking you may have a filter that is forcing mail to that folder. Moving mail from an IMAP account to a "local" folder inherently sees it deleted from the IMAP account as it is no longer there, hence it appearing in the deleted folder.

I think you may need to offer some more information on what junk filtering you have, perhaps facilitated by a third party product like an antivirus.

Lets start with the second item first. Welcome to the Microsoft freedom to innovate. Despite it not being included in the email specifications Microsoft in their corporate wisdom decided that if you send an email on their service you have to have a copy in your mail account. Hence Thunderbird makes a copy and so does Microsoft. Fun hey. But at least Thunderbird lets you turn of the copy in account settings > copies and folders. Microsoft offers no such setting. Now the first. It might be a little less straight forward. Generally speaking people use IMAP and with that changes are synchronized across multiple devices using the same account. SO in that situation deletions from say a phone will show up as you describe in Thunderbird as a mail appearing and them "just moving" somewhere else. That the mail is moving to a "local" junk folder leaves me thinking you may have a filter that is forcing mail to that folder. Moving mail from an IMAP account to a "local" folder inherently sees it deleted from the IMAP account as it is no longer there, hence it appearing in the deleted folder. I think you may need to offer some more information on what junk filtering you have, perhaps facilitated by a third party product like an antivirus.

Thank you for responding. By no means am I indicating that mozilla or thunderbird is at fault. If it came off that way, my bad. It's certainly some mess with microsoft because I don't have these problems with google emails in thunderbird.

I'm going to reinstall thunderbird and try it again using a less important email account. I don't really know what I've configured, but I don't think I have any third party antivirus enabled. I will report back.

Fault has nothing to do with it. It is just my long standing frustration with Microsoft speak glowing through.

I would expect a Google account in Thunderbird to have exactly the same sent mail duplication problem as they to joined the rush to ensure you never lost a sent mail, despite what the RFC says. Both require you to disable the Thunderbird copy to prevent duplication.

I don't think a reinstall will do anything useful at all, given that no settings are changed in the process. My guess is you have created some filters to manage spam and they are messing things up. But it is really only a guess.

Fault has nothing to do with it. It is just my long standing frustration with Microsoft speak glowing through. I would expect a Google account in Thunderbird to have exactly the same sent mail duplication problem as they to joined the rush to ensure you never lost a sent mail, despite what the RFC says. Both require you to disable the Thunderbird copy to prevent duplication. I don't think a reinstall will do anything useful at all, given that no settings are changed in the process. My guess is you have created some filters to manage spam and they are messing things up. But it is really only a guess.

The issue of multiple sent emails appearing in my sent folder does happen with gmail, but the issue of deleted emails doesn't happen with gmail. Is there a way for me to "reset" filters?

I had a similar problem with occasional deleted emails in thunderbird with an IMAP account. As a workaround, I turned off the option to move emails to the junk folder when marked as junk. This leaves them cluttering up the inbox, but it easy to scan them for mistakes, then use "delete mail marked as junk in folder" from the Tools menu. With this setup, I'm no longer losing emails.